We sometimes buy trout from a local breeder who'll get them fresh out of the water for us, and then cook them a few hours later. They taste great, but the flesh tends to fall apart in a way that doesn't happen with fish from the super market. It's often barely even possible to get them out of the pot without them completely coming apart. We tried leaving them in the fridge for a day so they wouldn't be quite as just-killed-an-hour-ago-fresh, but that didn't help.

We usually prepare them by cooking them in simmering (not boiling) water.

@baka: I edited my question to include that info.
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CassOct 1 '11 at 17:10

You cook the fish in water or trying to steam it? Steaming it would help tremendously since you do not need to remove the fish from the plate. A lot of chinese way of cooking fish is steaming
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HuangismJan 19 at 20:58

The best way to cook fresh fish is to put it into a plastic bag with as little air as possible (there are vacuum sealers available for that, but manually squeezing air out of the bag should work too), and place it in a water bath.

The plastic bag is necessary to prevent water access to fish while cooking. You need to keep temperature of that water at 132 Fahrenheit (55.5 Celsius), not less, not more (at 145F it'll already be overcooked). Depending on how thick is the piece it might take from ~20 minutes (half-inch thick) to couple hours (~2 inches thick) to make sure the entire piece was brought to this temperature (especially important if starting with not fresh, but frozen fish). After that you could just fry it for 30 seconds on each side to give it familiar "fried" (or use a propane torch from Home Depot) slightly "brown" look.

If you don't want to mess with plastic bags and keeping water temperature precise, still using a digital thermometer with a needle type sensor will help a lot in any cooking. The "doneness" of fish (and meat) depends only on what temperature you brought it during the process.

If currently you're simmering it — temperature is way above 132. It's most likely close to 220. Means — severely overcooked.

I am from the Bahamas and the way we keep fresh fish from falling apart is this:

After seasoning the fish, take a clean hand towel and gently tap the water off the fish until it's damp but not dry and be careful not to rub off the seasoning. Take a flat plate, sprinkle some flour on it and spread the flour to ensure it coats the entire plate. Take the damp fish by the tail and dip both sides of the fish in the plate of flour. Make sure the fish is lightly coated from head to tail.

Use a skillet filled with approximately 1/2 cup of oil and fry the coated fish on medium heat. When you notice the fish is slightly brown, turn the heat up and fry to a crisp golden brown. Add oil only as needed, too much oil will soften the fish and too little will cause it to stick. Watch the pot carefully and use a spatula to flip the fish. When flipping, make sure the spatula is in between the head and the body section.

This method is done before we cook the fish in any other form to prevent it falling apart. This is especially done before the fish is steamed, because it decreases the cooking time of the fish sitting in gravy, which causes it to fall apart if cooked for a long period of time.